You know, the fact that Mewtwo is put back into the spotlight this generation makes me a bit jaded because the time to do it would have been during Black and White. The reason for this is because Team Plasma, though they were ultimately faking, are a Pokemon rights group. In the anime, the only previous times in which the subject of Pokemon freedom is brought up that I can think of is with Mewtwo. Also, since Mewtwo is implied to be watching over a city like a vigilante or something, it would make sense to reveal his new home to be Unova. Then you could have had a thing where he allies with Team Plasma for a bit until he learns they're hypocrites, but ultimately befriends N because he's a true believer, etc, etc.
Missed opportunity, in my book. The fact that they're finally bringing Mewtwo back this generation as an entirely separate character just makes me think it was a thoughtless marketing decision. "Welp, we need a 'face' for the new generation. I know, just redesign Mewtwo, and give some reason for it to be in current events. The kids will love it, and the old fans will love it. DOUBLE DOLLARS."